Starting phenix.real_space_refine
on Thu Mar  5 02:03:18 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xzz_33535/03_2026/7xzz_33535.map"
  }
  resolution = 4.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     309      5.49       5
     S      78      5.16       5
     C   10646      2.51       5
     N    3495      2.21       5
     O    4095      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18623
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3164
          Classifications: {'DNA': 155}
          Link IDs: {'rna3p': 154}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen planarities: 2
    Chain: "J"
      Number of atoms: 3183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 3183
          Classifications: {'DNA': 155}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 154}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen planarities: 3
    Chain: "K"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1555
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 14, 'TRANS': 183}
    Chain: "L"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1555
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 14, 'TRANS': 183}
    Chain: "M"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1555
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 14, 'TRANS': 183}
    Chain: "N"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1555
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 14, 'TRANS': 183}
  Time building chain proxies: 3.66, per 1000 atoms: 0.20
  Number of scatterers: 18623
  At special positions: 0
  Unit cell: (159, 179.14, 120.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      78     16.00
     P     309     15.00
     O    4095      8.00
     N    3495      7.00
     C   10646      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 510.9 milliseconds
  

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2900

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 18 sheets defined
      42.9% alpha, 15.2% beta
      149 base pairs and 265 stacking pairs defined.
    Time for finding SS restraints: 2.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.096A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.293A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.117A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.995A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.538A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.553A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.880A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.269A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.524A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 122
    Processing helix  chain 'K' and resid 165 through 169
    Processing helix  chain 'K' and resid 176 through 182
    Processing helix  chain 'K' and resid 277 through 288
    Processing helix  chain 'K' and resid 289 through 291
      No H-bonds generated for 'chain 'K' and resid 289 through 291'
    Processing helix  chain 'L' and resid 165 through 169
    Processing helix  chain 'L' and resid 176 through 182
    Processing helix  chain 'L' and resid 277 through 288
    Processing helix  chain 'L' and resid 289 through 291
      No H-bonds generated for 'chain 'L' and resid 289 through 291'
    Processing helix  chain 'M' and resid 165 through 169
    Processing helix  chain 'M' and resid 176 through 182
    Processing helix  chain 'M' and resid 277 through 289
    Processing helix  chain 'N' and resid 165 through 169
    Processing helix  chain 'N' and resid 176 through 182
    Processing helix  chain 'N' and resid 277 through 288
    Processing helix  chain 'N' and resid 289 through 291
      No H-bonds generated for 'chain 'N' and resid 289 through 291'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.999A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.082A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
      removed outlier: 3.757A  pdb=" N   ILE C  78 " --> pdb=" O   GLY D  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.501A  pdb=" N   TYR F  98 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.760A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.342A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
      removed outlier: 3.547A  pdb=" N   ILE G  78 " --> pdb=" O   GLY H  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'K' and resid 110 through 112
    Processing sheet with id=AB3, first strand: chain 'K' and resid 124 through 127
      removed outlier: 6.213A  pdb=" N   LEU K 257 " --> pdb=" O   LEU K 265 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ARG K 267 " --> pdb=" O   ILE K 255 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   ILE K 255 " --> pdb=" O   ARG K 267 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   SER K 269 " --> pdb=" O   THR K 253 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   THR K 253 " --> pdb=" O   SER K 269 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLU K 271 " --> pdb=" O   ILE K 251 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE K 251 " --> pdb=" O   GLU K 271 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   ALA K 161 " --> pdb=" O   HIS K 214 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   HIS K 214 " --> pdb=" O   ALA K 161 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 110 through 112
    Processing sheet with id=AB5, first strand: chain 'L' and resid 124 through 127
      removed outlier: 3.803A  pdb=" N   ILE L 251 " --> pdb=" O   VAL L 272 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   ALA L 161 " --> pdb=" O   HIS L 214 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   HIS L 214 " --> pdb=" O   ALA L 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'M' and resid 110 through 112
    Processing sheet with id=AB7, first strand: chain 'M' and resid 124 through 127
      removed outlier: 3.832A  pdb=" N   ILE M 251 " --> pdb=" O   VAL M 272 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   ALA M 161 " --> pdb=" O   HIS M 214 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   HIS M 214 " --> pdb=" O   ALA M 161 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 110 through 112
    Processing sheet with id=AB9, first strand: chain 'N' and resid 124 through 127
      removed outlier: 3.839A  pdb=" N   ILE N 251 " --> pdb=" O   VAL N 272 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   ALA N 161 " --> pdb=" O   HIS N 214 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   HIS N 214 " --> pdb=" O   ALA N 161 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1767 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      385 hydrogen bonds
      762 hydrogen bond angles
      0 basepair planarities
      149 basepair parallelities
      265 stacking parallelities
  Total time for adding SS restraints: 3.49

  Time building geometry restraints manager: 2.00 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 3607
        1.33 -     1.46: 6509
        1.46 -     1.59: 8773
        1.59 -     1.71: 615
        1.71 -     1.84: 112
  Bond restraints: 19616
  Sorted by residual:
  bond pdb=" C   PRO L 222 "
       pdb=" O   PRO L 222 "
    ideal  model  delta    sigma   weight residual
    1.246  1.213  0.033 8.50e-03 1.38e+04 1.48e+01
  bond pdb=" C   PRO M 222 "
       pdb=" O   PRO M 222 "
    ideal  model  delta    sigma   weight residual
    1.240  1.202  0.039 1.12e-02 7.97e+03 1.19e+01
  bond pdb=" CA  PRO K 190 "
       pdb=" C   PRO K 190 "
    ideal  model  delta    sigma   weight residual
    1.514  1.533 -0.019 5.50e-03 3.31e+04 1.15e+01
  bond pdb=" N   VAL K 122 "
       pdb=" CA  VAL K 122 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.19e-02 7.06e+03 1.08e+01
  bond pdb=" N   VAL N 225 "
       pdb=" CA  VAL N 225 "
    ideal  model  delta    sigma   weight residual
    1.461  1.501 -0.040 1.24e-02 6.50e+03 1.06e+01
  ... (remaining 19611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 25847
        1.73 -     3.45: 1783
        3.45 -     5.18: 182
        5.18 -     6.91: 25
        6.91 -     8.63: 3
  Bond angle restraints: 27840
  Sorted by residual:
  angle pdb=" O   PRO L 190 "
        pdb=" C   PRO L 190 "
        pdb=" N   PRO L 191 "
      ideal   model   delta    sigma   weight residual
     121.31  123.33   -2.02 4.60e-01 4.73e+00 1.94e+01
  angle pdb=" N   LEU M 265 "
        pdb=" CA  LEU M 265 "
        pdb=" C   LEU M 265 "
      ideal   model   delta    sigma   weight residual
     113.88  108.67    5.21 1.23e+00 6.61e-01 1.79e+01
  angle pdb=" O   PRO M 190 "
        pdb=" C   PRO M 190 "
        pdb=" N   PRO M 191 "
      ideal   model   delta    sigma   weight residual
     121.31  123.17   -1.86 4.60e-01 4.73e+00 1.64e+01
  angle pdb=" N   GLN E  76 "
        pdb=" CA  GLN E  76 "
        pdb=" CB  GLN E  76 "
      ideal   model   delta    sigma   weight residual
     110.32  117.15   -6.83 1.70e+00 3.46e-01 1.61e+01
  angle pdb=" O3'  DG I 130 "
        pdb=" C3'  DG I 130 "
        pdb=" C2'  DG I 130 "
      ideal   model   delta    sigma   weight residual
     111.50  105.57    5.93 1.50e+00 4.44e-01 1.56e+01
  ... (remaining 27835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.69: 9129
       30.69 -    61.38: 1874
       61.38 -    92.07: 67
       92.07 -   122.76: 1
      122.76 -   153.45: 1
  Dihedral angle restraints: 11072
    sinusoidal: 6568
      harmonic: 4504
  Sorted by residual:
  dihedral pdb=" C4'  DC J  33 "
           pdb=" C3'  DC J  33 "
           pdb=" O3'  DC J  33 "
           pdb=" P    DC J  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.55  153.45     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" CA  TYR M 236 "
           pdb=" C   TYR M 236 "
           pdb=" N   MET M 237 "
           pdb=" CA  MET M 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.76  -18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  TYR K 236 "
           pdb=" C   TYR K 236 "
           pdb=" N   MET K 237 "
           pdb=" CA  MET K 237 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.63  -17.37     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 11069 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2240
       0.052 -    0.103: 618
       0.103 -    0.155: 175
       0.155 -    0.206: 78
       0.206 -    0.258: 8
  Chirality restraints: 3119
  Sorted by residual:
  chirality pdb=" CA  ARG L 248 "
            pdb=" N   ARG L 248 "
            pdb=" C   ARG L 248 "
            pdb=" CB  ARG L 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ARG N 248 "
            pdb=" N   ARG N 248 "
            pdb=" C   ARG N 248 "
            pdb=" CB  ARG N 248 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  GLU C  61 "
            pdb=" N   GLU C  61 "
            pdb=" C   GLU C  61 "
            pdb=" CB  GLU C  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.32e+00
  ... (remaining 3116 not shown)

  Planarity restraints: 2501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  52 "   -0.022 2.00e-02 2.50e+03   4.45e-02 1.98e+01
        pdb=" C   ALA G  52 "    0.077 2.00e-02 2.50e+03
        pdb=" O   ALA G  52 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ALA G  53 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.27e+00
        pdb=" C   LYS F  59 "    0.053 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   VAL F  60 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA J  19 "    0.030 2.00e-02 2.50e+03   1.26e-02 4.36e+00
        pdb=" N9   DA J  19 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA J  19 "   -0.009 2.00e-02 2.50e+03
        pdb=" N7   DA J  19 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DA J  19 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DA J  19 "    0.007 2.00e-02 2.50e+03
        pdb=" N6   DA J  19 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DA J  19 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA J  19 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DA J  19 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DA J  19 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 2498 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 37
        2.35 -     2.99: 9024
        2.99 -     3.63: 30316
        3.63 -     4.26: 49078
        4.26 -     4.90: 72886
  Nonbonded interactions: 161341
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU G  23 "
            pdb=" OE1 GLU G  56 "
     model   vdw
     1.717 3.460
  nonbonded pdb=" NH2 ARG G  17 "
            pdb=" OP2  DA J  55 "
     model   vdw
     1.839 3.120
  nonbonded pdb=" NH2 ARG K 202 "
            pdb=" OE2 GLU K 221 "
     model   vdw
     1.930 3.120
  nonbonded pdb=" NH2 ARG F  36 "
            pdb=" OP1  DA J  85 "
     model   vdw
     1.962 3.120
  nonbonded pdb=" NH2 ARG G  42 "
            pdb=" O4'  DT I 110 "
     model   vdw
     1.980 3.120
  ... (remaining 161336 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 121)
  selection = (chain 'H' and resid 28 through 121)
}
ncs_group {
  reference = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.590
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4393
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  19616  Z= 0.342
  Angle     :  0.915   8.632  27840  Z= 0.608
  Chirality :  0.057   0.258   3119
  Planarity :  0.005   0.045   2501
  Dihedral  : 25.147 153.453   8172
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.82 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.19), residues: 1530
  helix:  0.79 (0.18), residues: 629
  sheet:  0.45 (0.26), residues: 312
  loop :  0.30 (0.25), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M 267 
 TYR   0.026   0.003   TYR B  88 
 PHE   0.018   0.002   PHE N 270 
 TRP   0.004   0.002   TRP N 146 
 HIS   0.010   0.002   HIS K 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00582 (19616)
  covalent geometry    : angle       0.91516 (27840)
  hydrogen bonds       : bond        0.11363 ( 1015)
  hydrogen bonds       : angle       5.24993 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 261
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8591 (mt) cc_final: 0.8294 (mt)
REVERT: A  106 ASP cc_start: 0.8379 (m-30) cc_final: 0.7712 (m-30)
REVERT: C   83 LEU cc_start: 0.9529 (mt) cc_final: 0.9047 (mt)
REVERT: C   90 ASP cc_start: 0.8989 (t0) cc_final: 0.8760 (t0)
REVERT: E  106 ASP cc_start: 0.8567 (m-30) cc_final: 0.7538 (m-30)
REVERT: F   68 ASP cc_start: 0.8981 (m-30) cc_final: 0.8700 (p0)
REVERT: F   97 LEU cc_start: 0.8977 (tp) cc_final: 0.8683 (tt)
REVERT: G   38 ASN cc_start: 0.8115 (m-40) cc_final: 0.7859 (t0)
REVERT: G   56 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8229 (mt-10)
REVERT: G   64 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8154 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1414
  time to fit residues: 54.7416
Evaluate side-chains
  140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.0070
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 149 optimal weight:    0.0470
   overall best weight:    1.8102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** G  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
K 178 HIS
K 268 ASN
K 288 ASN
L 268 ASN
L 288 ASN
M 288 ASN
N 168 HIS
N 268 ASN
N 288 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.081693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.046082 restraints weight = 127724.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.046959 restraints weight = 59539.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.047118 restraints weight = 37341.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.047566 restraints weight = 29538.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.047739 restraints weight = 24413.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  19616  Z= 0.179
  Angle     :  0.630   9.783  27840  Z= 0.362
  Chirality :  0.040   0.229   3119
  Planarity :  0.005   0.069   2501
  Dihedral  : 28.992 156.499   5115
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.41 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.20), residues: 1530
  helix:  1.65 (0.19), residues: 625
  sheet:  0.55 (0.26), residues: 328
  loop :  0.58 (0.25), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  95 
 TYR   0.018   0.002   TYR F  88 
 PHE   0.028   0.002   PHE G  25 
 TRP   0.009   0.002   TRP L 146 
 HIS   0.007   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (19616)
  covalent geometry    : angle       0.62978 (27840)
  hydrogen bonds       : bond        0.04955 ( 1015)
  hydrogen bonds       : angle       4.10745 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9645 (mm-30) cc_final: 0.9417 (mm-30)
REVERT: A   84 PHE cc_start: 0.9044 (m-80) cc_final: 0.8822 (m-80)
REVERT: A   90 MET cc_start: 0.9613 (mmm) cc_final: 0.9363 (mmm)
REVERT: A   93 GLN cc_start: 0.9409 (tt0) cc_final: 0.8875 (tp40)
REVERT: A  106 ASP cc_start: 0.8975 (m-30) cc_final: 0.8443 (t70)
REVERT: B   68 ASP cc_start: 0.9039 (m-30) cc_final: 0.8682 (m-30)
REVERT: C   90 ASP cc_start: 0.8756 (t0) cc_final: 0.8422 (t0)
REVERT: C  102 ILE cc_start: 0.9394 (mm) cc_final: 0.9131 (mp)
REVERT: E   67 PHE cc_start: 0.9361 (t80) cc_final: 0.8295 (t80)
REVERT: E   92 LEU cc_start: 0.9657 (mt) cc_final: 0.9260 (tt)
REVERT: E   94 GLU cc_start: 0.9028 (tp30) cc_final: 0.8454 (tp30)
REVERT: E  103 LEU cc_start: 0.9678 (tt) cc_final: 0.9451 (pp)
REVERT: E  106 ASP cc_start: 0.8609 (m-30) cc_final: 0.8270 (m-30)
REVERT: G   38 ASN cc_start: 0.8681 (m-40) cc_final: 0.7988 (t0)
REVERT: G   64 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8782 (tm-30)
REVERT: G   90 ASP cc_start: 0.8416 (t70) cc_final: 0.8110 (t0)
REVERT: H   59 MET cc_start: 0.9734 (tpp) cc_final: 0.9302 (mmp)
REVERT: K  193 HIS cc_start: 0.1150 (t-90) cc_final: 0.0748 (t-90)
REVERT: K  246 MET cc_start: -0.0449 (mtt) cc_final: -0.0937 (mtm)
REVERT: M  224 GLU cc_start: 0.1756 (mp0) cc_final: 0.1177 (pm20)
REVERT: N  237 MET cc_start: 0.8052 (mmm) cc_final: 0.7623 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 184
  average time/residue: 0.1443
  time to fit residues: 40.1726
Evaluate side-chains
  131 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 155 optimal weight:   40.0000
   chunk 87 optimal weight:   60.0000
   chunk 14 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 79 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 75 optimal weight:    8.9990
   chunk 112 optimal weight:   20.0000
   chunk 131 optimal weight:   50.0000
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
** G  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
K 100 GLN
K 178 HIS
K 239 ASN
M 193 HIS
N 168 HIS
N 214 HIS
N 239 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.077081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.041034 restraints weight = 131552.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.041593 restraints weight = 60762.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.041718 restraints weight = 37298.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.042098 restraints weight = 29200.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.042409 restraints weight = 24978.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117  19616  Z= 0.236
  Angle     :  0.625   8.285  27840  Z= 0.364
  Chirality :  0.040   0.212   3119
  Planarity :  0.005   0.048   2501
  Dihedral  : 29.015 158.304   5115
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  2.97 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.20), residues: 1530
  helix:  1.66 (0.20), residues: 630
  sheet:  0.88 (0.28), residues: 304
  loop :  0.60 (0.25), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  72 
 TYR   0.040   0.002   TYR B  88 
 PHE   0.019   0.002   PHE G  25 
 TRP   0.008   0.001   TRP K 146 
 HIS   0.017   0.002   HIS K 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (19616)
  covalent geometry    : angle       0.62488 (27840)
  hydrogen bonds       : bond        0.05587 ( 1015)
  hydrogen bonds       : angle       4.11170 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9672 (mm-30) cc_final: 0.9437 (mm-30)
REVERT: A  120 MET cc_start: 0.8673 (mmp) cc_final: 0.8395 (mmm)
REVERT: B   63 GLU cc_start: 0.9468 (mt-10) cc_final: 0.9258 (pp20)
REVERT: B   66 ILE cc_start: 0.9743 (mm) cc_final: 0.9521 (tt)
REVERT: B   84 MET cc_start: 0.9333 (tpt) cc_final: 0.9025 (tpp)
REVERT: C   87 ILE cc_start: 0.9774 (OUTLIER) cc_final: 0.9473 (tp)
REVERT: C   90 ASP cc_start: 0.8818 (t0) cc_final: 0.8505 (t0)
REVERT: D  110 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8557 (mt-10)
REVERT: E   92 LEU cc_start: 0.9590 (mt) cc_final: 0.9354 (tp)
REVERT: E   96 CYS cc_start: 0.9505 (m) cc_final: 0.9247 (m)
REVERT: E  106 ASP cc_start: 0.8840 (m-30) cc_final: 0.8619 (m-30)
REVERT: E  120 MET cc_start: 0.8507 (mmp) cc_final: 0.8294 (mmm)
REVERT: F   63 GLU cc_start: 0.9569 (mt-10) cc_final: 0.9233 (mt-10)
REVERT: G   38 ASN cc_start: 0.9109 (m-40) cc_final: 0.8173 (t0)
REVERT: G   64 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8919 (tm-30)
REVERT: G   75 LYS cc_start: 0.8429 (mmpt) cc_final: 0.8165 (mmmm)
REVERT: G   90 ASP cc_start: 0.8584 (t70) cc_final: 0.8248 (t70)
REVERT: H   59 MET cc_start: 0.9823 (tpp) cc_final: 0.9477 (mmp)
REVERT: N  237 MET cc_start: 0.7818 (mmm) cc_final: 0.7513 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1503
  time to fit residues: 37.0233
Evaluate side-chains
  123 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 165 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 171 optimal weight:    8.9990
   chunk 172 optimal weight:   50.0000
   chunk 175 optimal weight:    5.9990
   chunk 169 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    4.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  60 ASN
** G  68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
K 235 ASN
L 168 HIS
L 239 ASN
M 178 HIS
M 214 HIS
M 239 ASN
N 168 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.073296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.037552 restraints weight = 133298.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.038085 restraints weight = 64010.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.038194 restraints weight = 38853.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.038353 restraints weight = 29457.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.038330 restraints weight = 24800.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.151  19616  Z= 0.270
  Angle     :  0.667   8.918  27840  Z= 0.381
  Chirality :  0.041   0.212   3119
  Planarity :  0.005   0.046   2501
  Dihedral  : 29.252 163.829   5115
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  3.19 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.21), residues: 1530
  helix:  1.41 (0.19), residues: 629
  sheet:  0.89 (0.28), residues: 304
  loop :  0.40 (0.25), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  77 
 TYR   0.047   0.002   TYR H  80 
 PHE   0.023   0.002   PHE A  67 
 TRP   0.008   0.001   TRP K 146 
 HIS   0.010   0.002   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00599 (19616)
  covalent geometry    : angle       0.66661 (27840)
  hydrogen bonds       : bond        0.05951 ( 1015)
  hydrogen bonds       : angle       4.14231 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.9272 (mtt90) cc_final: 0.8903 (ptp-170)
REVERT: A   84 PHE cc_start: 0.9294 (m-80) cc_final: 0.9034 (m-80)
REVERT: A   90 MET cc_start: 0.9728 (mmm) cc_final: 0.9520 (mmp)
REVERT: A  106 ASP cc_start: 0.9039 (m-30) cc_final: 0.8767 (m-30)
REVERT: A  120 MET cc_start: 0.8921 (mmp) cc_final: 0.8628 (mmm)
REVERT: B   63 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9164 (tp30)
REVERT: B   66 ILE cc_start: 0.9777 (mm) cc_final: 0.9534 (tt)
REVERT: B   68 ASP cc_start: 0.9317 (m-30) cc_final: 0.9003 (m-30)
REVERT: B   84 MET cc_start: 0.9505 (tpt) cc_final: 0.9101 (mmm)
REVERT: C   90 ASP cc_start: 0.8879 (t0) cc_final: 0.8512 (t0)
REVERT: D   65 ASP cc_start: 0.9318 (t0) cc_final: 0.9090 (t0)
REVERT: D  110 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8825 (mt-10)
REVERT: E   96 CYS cc_start: 0.9482 (m) cc_final: 0.9248 (m)
REVERT: E  106 ASP cc_start: 0.8922 (m-30) cc_final: 0.8709 (m-30)
REVERT: E  120 MET cc_start: 0.8867 (mmp) cc_final: 0.8472 (mmm)
REVERT: E  123 ASP cc_start: 0.8746 (m-30) cc_final: 0.8368 (m-30)
REVERT: G   64 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8964 (tm-30)
REVERT: G   90 ASP cc_start: 0.8369 (t70) cc_final: 0.8132 (t70)
REVERT: H   59 MET cc_start: 0.9832 (tpp) cc_final: 0.9522 (mmp)
REVERT: K  246 MET cc_start: -0.0019 (mtt) cc_final: -0.0419 (mtm)
REVERT: L  169 MET cc_start: 0.0265 (tpp) cc_final: -0.0102 (tpt)
REVERT: N  237 MET cc_start: 0.8036 (mmm) cc_final: 0.7770 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 150
  average time/residue: 0.1483
  time to fit residues: 33.6073
Evaluate side-chains
  111 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 171 optimal weight:    0.2980
   chunk 18 optimal weight:    8.9990
   chunk 138 optimal weight:   50.0000
   chunk 82 optimal weight:    7.9990
   chunk 130 optimal weight:    0.0770
   chunk 97 optimal weight:    5.9990
   chunk 136 optimal weight:   30.0000
   chunk 26 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 154 optimal weight:    5.9990
   overall best weight:    3.4744

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
A  93 GLN
C  24 GLN
G  68 ASN
** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 178 HIS
N 168 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.073718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.037021 restraints weight = 131999.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.037385 restraints weight = 61696.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.037538 restraints weight = 41340.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.038082 restraints weight = 33266.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.038138 restraints weight = 28329.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  19616  Z= 0.204
  Angle     :  0.603   9.730  27840  Z= 0.348
  Chirality :  0.039   0.177   3119
  Planarity :  0.004   0.049   2501
  Dihedral  : 29.266 163.720   5115
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.46 (0.21), residues: 1530
  helix:  1.65 (0.20), residues: 623
  sheet:  0.92 (0.28), residues: 304
  loop :  0.42 (0.25), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  30 
 TYR   0.019   0.001   TYR H  80 
 PHE   0.026   0.002   PHE A 104 
 TRP   0.005   0.001   TRP L 146 
 HIS   0.022   0.001   HIS M 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (19616)
  covalent geometry    : angle       0.60254 (27840)
  hydrogen bonds       : bond        0.04681 ( 1015)
  hydrogen bonds       : angle       3.87983 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9701 (mm-30) cc_final: 0.9456 (mm-30)
REVERT: A   52 ARG cc_start: 0.9265 (mtt90) cc_final: 0.8905 (ptt-90)
REVERT: A   94 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9011 (tp30)
REVERT: A  106 ASP cc_start: 0.9041 (m-30) cc_final: 0.8764 (m-30)
REVERT: B   43 VAL cc_start: 0.9482 (t) cc_final: 0.9257 (t)
REVERT: B   63 GLU cc_start: 0.9465 (mt-10) cc_final: 0.8918 (mm-30)
REVERT: B   66 ILE cc_start: 0.9778 (mm) cc_final: 0.9545 (tt)
REVERT: B   84 MET cc_start: 0.9477 (tpt) cc_final: 0.9116 (mmm)
REVERT: C   90 ASP cc_start: 0.8970 (t0) cc_final: 0.8582 (t0)
REVERT: D   65 ASP cc_start: 0.9284 (t0) cc_final: 0.9052 (t0)
REVERT: D  110 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8839 (mt-10)
REVERT: E  106 ASP cc_start: 0.8955 (m-30) cc_final: 0.8684 (m-30)
REVERT: E  120 MET cc_start: 0.8866 (mmp) cc_final: 0.8663 (mmm)
REVERT: F   84 MET cc_start: 0.9575 (mmp) cc_final: 0.9353 (tpp)
REVERT: G   64 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9052 (tm-30)
REVERT: G   75 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8500 (mmmm)
REVERT: H   59 MET cc_start: 0.9828 (tpp) cc_final: 0.9579 (mmm)
REVERT: K  246 MET cc_start: 0.0038 (mtt) cc_final: -0.0289 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1458
  time to fit residues: 31.4742
Evaluate side-chains
  113 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 170 optimal weight:    3.9990
   chunk 160 optimal weight:    7.9990
   chunk 175 optimal weight:   50.0000
   chunk 62 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 136 optimal weight:   30.0000
   chunk 154 optimal weight:   50.0000
   chunk 125 optimal weight:   40.0000
   chunk 32 optimal weight:    4.9990
   chunk 77 optimal weight:    7.9990
   chunk 146 optimal weight:   50.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D  60 ASN
G  68 ASN
** K 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 168 HIS
N 263 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.071469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.035826 restraints weight = 134871.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.036155 restraints weight = 65048.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.036362 restraints weight = 46395.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.036435 restraints weight = 33400.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.036405 restraints weight = 26522.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.119  19616  Z= 0.291
  Angle     :  0.660  12.089  27840  Z= 0.377
  Chirality :  0.041   0.158   3119
  Planarity :  0.005   0.048   2501
  Dihedral  : 29.378 168.144   5115
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.21), residues: 1530
  helix:  1.47 (0.20), residues: 630
  sheet:  0.87 (0.29), residues: 300
  loop :  0.35 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  72 
 TYR   0.024   0.002   TYR H  80 
 PHE   0.018   0.002   PHE A  67 
 TRP   0.004   0.001   TRP K 146 
 HIS   0.010   0.002   HIS M 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 (19616)
  covalent geometry    : angle       0.65998 (27840)
  hydrogen bonds       : bond        0.06396 ( 1015)
  hydrogen bonds       : angle       4.20574 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9669 (mm-30) cc_final: 0.9355 (mm-30)
REVERT: A   94 GLU cc_start: 0.9433 (mm-30) cc_final: 0.9183 (mm-30)
REVERT: A  106 ASP cc_start: 0.8987 (m-30) cc_final: 0.8739 (m-30)
REVERT: B   66 ILE cc_start: 0.9784 (mm) cc_final: 0.9555 (tt)
REVERT: B   74 GLU cc_start: 0.9533 (tm-30) cc_final: 0.9262 (tm-30)
REVERT: B   84 MET cc_start: 0.9573 (tpt) cc_final: 0.9319 (mmm)
REVERT: C   90 ASP cc_start: 0.9041 (t0) cc_final: 0.8700 (t70)
REVERT: D   65 ASP cc_start: 0.9358 (t0) cc_final: 0.9084 (t0)
REVERT: E   92 LEU cc_start: 0.9477 (tt) cc_final: 0.9257 (tt)
REVERT: E   96 CYS cc_start: 0.9395 (m) cc_final: 0.9122 (m)
REVERT: E  120 MET cc_start: 0.8882 (mmp) cc_final: 0.8406 (mmm)
REVERT: E  123 ASP cc_start: 0.8726 (m-30) cc_final: 0.8493 (m-30)
REVERT: G   64 GLU cc_start: 0.9279 (tm-30) cc_final: 0.9032 (tm-30)
REVERT: H   59 MET cc_start: 0.9836 (tpp) cc_final: 0.9610 (mmm)
REVERT: K  246 MET cc_start: 0.0192 (mtt) cc_final: -0.0038 (mtt)
REVERT: N  133 MET cc_start: 0.6804 (ppp) cc_final: 0.6504 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1342
  time to fit residues: 27.1241
Evaluate side-chains
  101 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 142 optimal weight:    0.7980
   chunk 145 optimal weight:    0.0770
   chunk 169 optimal weight:   40.0000
   chunk 46 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 121 optimal weight:    0.0980
   chunk 8 optimal weight:    3.9990
   chunk 168 optimal weight:   40.0000
   chunk 105 optimal weight:   50.0000
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G  68 ASN
N 168 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.074077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.036277 restraints weight = 132234.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.036719 restraints weight = 61686.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.036898 restraints weight = 40854.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.037380 restraints weight = 32402.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.037491 restraints weight = 27033.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.5415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  19616  Z= 0.144
  Angle     :  0.581   8.548  27840  Z= 0.335
  Chirality :  0.038   0.167   3119
  Planarity :  0.004   0.048   2501
  Dihedral  : 29.345 169.814   5115
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.21), residues: 1530
  helix:  1.69 (0.20), residues: 623
  sheet:  0.99 (0.29), residues: 300
  loop :  0.40 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG M 175 
 TYR   0.018   0.001   TYR H  80 
 PHE   0.034   0.001   PHE A 104 
 TRP   0.004   0.000   TRP K 146 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (19616)
  covalent geometry    : angle       0.58134 (27840)
  hydrogen bonds       : bond        0.04060 ( 1015)
  hydrogen bonds       : angle       3.76529 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9679 (mm-30) cc_final: 0.9378 (mm-30)
REVERT: A   74 ILE cc_start: 0.9470 (tt) cc_final: 0.9256 (tp)
REVERT: A   84 PHE cc_start: 0.9052 (m-80) cc_final: 0.8478 (m-80)
REVERT: A   94 GLU cc_start: 0.9439 (mm-30) cc_final: 0.9081 (mm-30)
REVERT: A  106 ASP cc_start: 0.9051 (m-30) cc_final: 0.8733 (m-30)
REVERT: A  120 MET cc_start: 0.8515 (mmp) cc_final: 0.8244 (mmm)
REVERT: B   43 VAL cc_start: 0.9504 (t) cc_final: 0.9017 (t)
REVERT: B   63 GLU cc_start: 0.9473 (mt-10) cc_final: 0.8934 (mm-30)
REVERT: B   66 ILE cc_start: 0.9789 (mm) cc_final: 0.9573 (tt)
REVERT: B   68 ASP cc_start: 0.9355 (m-30) cc_final: 0.9106 (m-30)
REVERT: B   74 GLU cc_start: 0.9481 (tm-30) cc_final: 0.9179 (tm-30)
REVERT: B   84 MET cc_start: 0.9442 (tpt) cc_final: 0.9009 (mmm)
REVERT: B   88 TYR cc_start: 0.9456 (m-10) cc_final: 0.9143 (m-80)
REVERT: C   90 ASP cc_start: 0.8892 (t0) cc_final: 0.8195 (t70)
REVERT: D   65 ASP cc_start: 0.9361 (t0) cc_final: 0.9110 (t0)
REVERT: E   97 GLU cc_start: 0.9067 (pm20) cc_final: 0.8755 (pm20)
REVERT: E  105 GLU cc_start: 0.9118 (pp20) cc_final: 0.8848 (pp20)
REVERT: E  106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8607 (m-30)
REVERT: E  120 MET cc_start: 0.8758 (mmp) cc_final: 0.8556 (mmm)
REVERT: E  123 ASP cc_start: 0.8702 (m-30) cc_final: 0.8469 (m-30)
REVERT: F   79 LYS cc_start: 0.9443 (mtpp) cc_final: 0.9151 (mtmm)
REVERT: F   84 MET cc_start: 0.9249 (tpp) cc_final: 0.8880 (tpp)
REVERT: G   64 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8982 (tm-30)
REVERT: G   68 ASN cc_start: 0.9091 (m-40) cc_final: 0.8805 (m-40)
REVERT: G   75 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8613 (mmmm)
REVERT: G   90 ASP cc_start: 0.8351 (t70) cc_final: 0.8113 (t0)
REVERT: H   59 MET cc_start: 0.9798 (tpp) cc_final: 0.9347 (mmm)
REVERT: K  246 MET cc_start: -0.0188 (mtt) cc_final: -0.0394 (mtt)
REVERT: N  133 MET cc_start: 0.6820 (ppp) cc_final: 0.6532 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1319
  time to fit residues: 30.7675
Evaluate side-chains
  113 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 133 optimal weight:   50.0000
   chunk 71 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 127 optimal weight:   30.0000
   chunk 144 optimal weight:   20.0000
   chunk 154 optimal weight:    8.9990
   chunk 64 optimal weight:    5.9990
   chunk 40 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
N 168 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.072885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.035966 restraints weight = 131983.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.036460 restraints weight = 63039.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.036975 restraints weight = 41815.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.037089 restraints weight = 31270.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.036836 restraints weight = 26979.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  19616  Z= 0.171
  Angle     :  0.579  10.642  27840  Z= 0.333
  Chirality :  0.038   0.159   3119
  Planarity :  0.004   0.051   2501
  Dihedral  : 29.215 172.457   5115
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.21), residues: 1530
  helix:  1.81 (0.20), residues: 628
  sheet:  0.98 (0.29), residues: 300
  loop :  0.44 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.016   0.001   TYR H  80 
 PHE   0.011   0.001   PHE F  61 
 TRP   0.004   0.001   TRP K 146 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (19616)
  covalent geometry    : angle       0.57938 (27840)
  hydrogen bonds       : bond        0.04380 ( 1015)
  hydrogen bonds       : angle       3.72616 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9347 (mm-30)
REVERT: A   74 ILE cc_start: 0.9541 (tt) cc_final: 0.9283 (tp)
REVERT: A   84 PHE cc_start: 0.9111 (m-80) cc_final: 0.8565 (m-80)
REVERT: A   94 GLU cc_start: 0.9649 (mm-30) cc_final: 0.8918 (mm-30)
REVERT: A   97 GLU cc_start: 0.9021 (pp20) cc_final: 0.8659 (pp20)
REVERT: A  106 ASP cc_start: 0.9067 (m-30) cc_final: 0.8564 (m-30)
REVERT: A  120 MET cc_start: 0.8706 (mmp) cc_final: 0.8399 (mmm)
REVERT: B   63 GLU cc_start: 0.9497 (mt-10) cc_final: 0.8951 (mm-30)
REVERT: B   66 ILE cc_start: 0.9796 (mm) cc_final: 0.9563 (tt)
REVERT: B   74 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9169 (tm-30)
REVERT: B   84 MET cc_start: 0.9490 (tpt) cc_final: 0.9157 (mmm)
REVERT: C   90 ASP cc_start: 0.8637 (t0) cc_final: 0.8266 (t0)
REVERT: E   92 LEU cc_start: 0.9436 (tt) cc_final: 0.9212 (tt)
REVERT: E   96 CYS cc_start: 0.9362 (m) cc_final: 0.9046 (m)
REVERT: E  103 LEU cc_start: 0.9503 (mm) cc_final: 0.9257 (mm)
REVERT: E  106 ASP cc_start: 0.8993 (m-30) cc_final: 0.8626 (m-30)
REVERT: F   74 GLU cc_start: 0.9622 (tm-30) cc_final: 0.9328 (tm-30)
REVERT: F   79 LYS cc_start: 0.9448 (mtpp) cc_final: 0.9118 (mtmm)
REVERT: G   64 GLU cc_start: 0.9278 (tm-30) cc_final: 0.8996 (tm-30)
REVERT: G   68 ASN cc_start: 0.9120 (m-40) cc_final: 0.8806 (m110)
REVERT: G   75 LYS cc_start: 0.8960 (mmpt) cc_final: 0.8690 (mmmm)
REVERT: G   90 ASP cc_start: 0.8345 (t70) cc_final: 0.8109 (t0)
REVERT: H   59 MET cc_start: 0.9779 (tpp) cc_final: 0.9337 (mmm)
REVERT: K  246 MET cc_start: 0.0147 (mtt) cc_final: -0.0105 (mtt)
REVERT: N  133 MET cc_start: 0.6826 (ppp) cc_final: 0.6573 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1368
  time to fit residues: 29.3546
Evaluate side-chains
  109 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   chunk 109 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 128 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 147 optimal weight:    5.9990
   chunk 145 optimal weight:   20.0000
   chunk 153 optimal weight:   50.0000
   chunk 13 optimal weight:    0.9980
   overall best weight:    5.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D  46 HIS
D  60 ASN
G  68 ASN
N 168 HIS
N 233 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.069996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.033601 restraints weight = 139264.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.033906 restraints weight = 71095.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.034400 restraints weight = 47681.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.034408 restraints weight = 36316.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.034655 restraints weight = 31416.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.6183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.109  19616  Z= 0.299
  Angle     :  0.671  15.076  27840  Z= 0.377
  Chirality :  0.041   0.151   3119
  Planarity :  0.005   0.051   2501
  Dihedral  : 29.421 178.084   5115
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.21), residues: 1530
  helix:  1.46 (0.20), residues: 630
  sheet:  0.90 (0.29), residues: 300
  loop :  0.45 (0.26), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG L 248 
 TYR   0.023   0.002   TYR H  80 
 PHE   0.016   0.002   PHE A  67 
 TRP   0.005   0.001   TRP M 146 
 HIS   0.009   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00653 (19616)
  covalent geometry    : angle       0.67055 (27840)
  hydrogen bonds       : bond        0.06814 ( 1015)
  hydrogen bonds       : angle       4.13211 ( 2529)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9688 (mm-30) cc_final: 0.9417 (mm-30)
REVERT: A   74 ILE cc_start: 0.9514 (tt) cc_final: 0.9302 (tp)
REVERT: A   94 GLU cc_start: 0.9613 (mm-30) cc_final: 0.8956 (mm-30)
REVERT: A   97 GLU cc_start: 0.9062 (pp20) cc_final: 0.8617 (pp20)
REVERT: A  106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8534 (m-30)
REVERT: A  120 MET cc_start: 0.8684 (mmp) cc_final: 0.8407 (mmm)
REVERT: B   63 GLU cc_start: 0.9523 (mt-10) cc_final: 0.9012 (mm-30)
REVERT: B   66 ILE cc_start: 0.9784 (mm) cc_final: 0.9530 (tt)
REVERT: B   74 GLU cc_start: 0.9547 (tm-30) cc_final: 0.9282 (tm-30)
REVERT: B   84 MET cc_start: 0.9572 (tpt) cc_final: 0.9285 (mmm)
REVERT: C   90 ASP cc_start: 0.8832 (t0) cc_final: 0.8523 (t70)
REVERT: E   96 CYS cc_start: 0.9354 (m) cc_final: 0.9113 (m)
REVERT: E  103 LEU cc_start: 0.9546 (mm) cc_final: 0.9289 (mm)
REVERT: E  106 ASP cc_start: 0.9288 (m-30) cc_final: 0.8615 (m-30)
REVERT: E  120 MET cc_start: 0.8694 (mmp) cc_final: 0.8171 (mmm)
REVERT: E  123 ASP cc_start: 0.8753 (m-30) cc_final: 0.8353 (m-30)
REVERT: F   74 GLU cc_start: 0.9668 (tm-30) cc_final: 0.9367 (tm-30)
REVERT: F   79 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9057 (mtpt)
REVERT: F   84 MET cc_start: 0.9381 (tpp) cc_final: 0.9094 (tpp)
REVERT: G   90 ASP cc_start: 0.8328 (t70) cc_final: 0.8110 (t70)
REVERT: H   59 MET cc_start: 0.9846 (tpp) cc_final: 0.9371 (mmm)
REVERT: K  246 MET cc_start: 0.0986 (mtt) cc_final: 0.0734 (mtt)
REVERT: N  133 MET cc_start: 0.6802 (ppp) cc_final: 0.6561 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1362
  time to fit residues: 25.7566
Evaluate side-chains
  93 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 146 optimal weight:   40.0000
   chunk 83 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 101 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
H  60 ASN
** K 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 168 HIS
N 233 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.070591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.034389 restraints weight = 134230.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.034616 restraints weight = 65739.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.034822 restraints weight = 41082.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.035055 restraints weight = 31458.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.035092 restraints weight = 27196.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.6561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.101  19616  Z= 0.257
  Angle     :  0.641  12.889  27840  Z= 0.366
  Chirality :  0.040   0.163   3119
  Planarity :  0.004   0.051   2501
  Dihedral  : 29.603 175.450   5115
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.31 (0.21), residues: 1530
  helix:  1.48 (0.20), residues: 626
  sheet:  0.86 (0.29), residues: 300
  loop :  0.39 (0.26), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 213 
 TYR   0.019   0.001   TYR H  80 
 PHE   0.015   0.001   PHE A  67 
 TRP   0.004   0.001   TRP K 146 
 HIS   0.008   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 (19616)
  covalent geometry    : angle       0.64072 (27840)
  hydrogen bonds       : bond        0.05007 ( 1015)
  hydrogen bonds       : angle       4.08263 ( 2529)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.9687 (mm-30) cc_final: 0.9440 (mm-30)
REVERT: A   74 ILE cc_start: 0.9485 (tt) cc_final: 0.9261 (tp)
REVERT: A   94 GLU cc_start: 0.9615 (mm-30) cc_final: 0.8955 (mm-30)
REVERT: A   97 GLU cc_start: 0.9002 (pp20) cc_final: 0.8643 (pp20)
REVERT: A  106 ASP cc_start: 0.9065 (m-30) cc_final: 0.8581 (m-30)
REVERT: A  120 MET cc_start: 0.8543 (mmp) cc_final: 0.8158 (mmm)
REVERT: B   63 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9003 (mm-30)
REVERT: B   66 ILE cc_start: 0.9780 (mm) cc_final: 0.9519 (tt)
REVERT: B   74 GLU cc_start: 0.9557 (tm-30) cc_final: 0.9286 (tm-30)
REVERT: B   84 MET cc_start: 0.9545 (tpt) cc_final: 0.9229 (mmm)
REVERT: C   90 ASP cc_start: 0.8951 (t0) cc_final: 0.8581 (t70)
REVERT: E   92 LEU cc_start: 0.9423 (tt) cc_final: 0.9210 (tt)
REVERT: E   96 CYS cc_start: 0.9367 (m) cc_final: 0.9147 (m)
REVERT: E  103 LEU cc_start: 0.9567 (mm) cc_final: 0.9343 (mm)
REVERT: E  106 ASP cc_start: 0.9007 (m-30) cc_final: 0.8781 (m-30)
REVERT: E  120 MET cc_start: 0.8651 (mmp) cc_final: 0.8109 (mmm)
REVERT: E  123 ASP cc_start: 0.8684 (m-30) cc_final: 0.8283 (m-30)
REVERT: F   74 GLU cc_start: 0.9677 (tm-30) cc_final: 0.9369 (tm-30)
REVERT: F   84 MET cc_start: 0.9279 (tpp) cc_final: 0.8972 (tpp)
REVERT: G   90 ASP cc_start: 0.8278 (t70) cc_final: 0.8070 (t0)
REVERT: H   59 MET cc_start: 0.9850 (tpp) cc_final: 0.9391 (mmm)
REVERT: K  236 TYR cc_start: 0.5161 (m-80) cc_final: 0.4944 (m-80)
REVERT: K  246 MET cc_start: 0.1227 (mtt) cc_final: 0.0927 (mtt)
REVERT: N  133 MET cc_start: 0.6776 (ppp) cc_final: 0.6537 (ppp)
REVERT: N  237 MET cc_start: 0.8093 (mmm) cc_final: 0.7836 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1377
  time to fit residues: 25.5169
Evaluate side-chains
  91 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 178
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 147 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0270
   chunk 69 optimal weight:    0.6980
   chunk 18 optimal weight:   20.0000
   overall best weight:    0.7442

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
F  27 GLN
G  68 ASN
H  60 ASN
K 178 HIS
K 214 HIS
N 168 HIS
N 233 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.072904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.035644 restraints weight = 132005.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.036274 restraints weight = 62885.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.036430 restraints weight = 40068.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.036804 restraints weight = 31559.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.036859 restraints weight = 26974.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.6556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  19616  Z= 0.140
  Angle     :  0.585   9.043  27840  Z= 0.332
  Chirality :  0.038   0.167   3119
  Planarity :  0.004   0.054   2501
  Dihedral  : 29.397 176.571   5115
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.21), residues: 1530
  helix:  1.77 (0.20), residues: 625
  sheet:  0.84 (0.29), residues: 300
  loop :  0.42 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  92 
 TYR   0.013   0.001   TYR H  80 
 PHE   0.011   0.001   PHE G  25 
 TRP   0.004   0.001   TRP N 146 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (19616)
  covalent geometry    : angle       0.58452 (27840)
  hydrogen bonds       : bond        0.03951 ( 1015)
  hydrogen bonds       : angle       3.68909 ( 2529)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5297.47 seconds
wall clock time: 91 minutes 16.38 seconds (5476.38 seconds total)